Commit eabf7ce7 authored by mcariou's avatar mcariou
Browse files

rerun primates

parent 3697116a
......@@ -62,8 +62,6 @@ y=as.numeric(as.character(outlier$bats_omegaM0codeml)),
outlier$Gene.name)
@
\subsection{Cooper-bats VS Hawkins-bats and DGINN-bats VS Hawkins-bats}
\section{Overlap}
\subsection{Data}
......@@ -159,11 +157,8 @@ dftmp<-tab[,c("bats_File", "bats_Name",
names(dftmp)<-names(df)
makeFig1(dftmp)
@
\end{document}
......
......@@ -30,108 +30,166 @@
Analysis were formatted by the script covid\_comp\_script0\_table.Rnw.
<<>>=
workdir<-"/home/adminmarie/Documents/CIRI_BIBS_projects/2020_05_Etienne_covid/"
home<-"/home/adminmarie/Documents/"
workdir<-paste0(home, "CIRI_BIBS_projects/2020_05_Etienne_covid/")
tab<-read.delim(paste0(workdir,
"covid_comp/covid_comp_complete.txt"), h=T, sep="\t")
dim(tab)
tab$Gene.name<-as.character(tab$Gene.name)
tab$Gene.name<-as.character(tab$Gene.name.x)
tab$Gene.name[tab$PreyGene=="MTARC1"]<-"MTARC1"
@
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\section{Comparisons Primates}
\subsection{Janet Young's results (Young-primate) VS DGINN-full's results}
Comparaison des Omega: colonne L "whole.gene.dN.dS.model.0" VS colonne "omega" dans la sortie de dginn.
<<omegaM7M8_1>>=
plot(tab$whole.gene.dN.dS.model.0, as.numeric(as.character(tab$dginn.primate_omegaM0Bpp)),
xlab="Omega Young-primate", ylab="DGINN-full's")
<<omegaM7M8_1>>=
tab$dginn.primate_omegaM0Bpp[tab$dginn.primate_omegaM0Bpp=="na"]<-NA
tab$dginn.primate_omegaM0Bpp<-as.numeric(as.character(
tab$dginn.primate_omegaM0Bpp))
plot(tab$whole.gene.dN.dS.model.0,
tab$dginn.primate_omegaM0Bpp,
xlab="Omega Young-primate",
ylab="DGINN-full's",
cex=0.3)
abline(0,1)
abline(lm(as.numeric(as.character(tab$dginn.primate_omegaM0Bpp))~tab$whole.gene.dN.dS.model.0), col="red")
abline(lm(tab$dginn.primate_omegaM0Bpp~tab$whole.gene.dN.dS.model.0),
col="red")
outlier<-tab[tab$whole.gene.dN.dS.model.0<0.4 & tab$dginn.primate_omegaM0Bpp>0.5,]
outlier<-tab[tab$whole.gene.dN.dS.model.0<0.4 &
tab$dginn.primate_omegaM0Bpp>0.5,]
text(x=outlier$whole.gene.dN.dS.model.0,
y=outlier$dginn.primate_omegaM0Bpp,
outlier$Gene.name)
outlier<-tab[tab$whole.gene.dN.dS.model.0<0.1 &
tab$dginn.primate_omegaM0Bpp>0.3,]
text(x=outlier$whole.gene.dN.dS.model.0,
y=outlier$dginn.primate_omegaM0Bpp,
outlier$Gene.name)
outlier<-tab[tab$whole.gene.dN.dS.model.0>0.33 &
tab$dginn.primate_omegaM0Bpp<0.2,]
text(x=outlier$whole.gene.dN.dS.model.0,
y=outlier$dginn.primate_omegaM0Bpp,
outlier$Gene.name)
outlier<-tab[tab$whole.gene.dN.dS.model.0>0.6 &
tab$dginn.primate_omegaM0Bpp<0.6,]
text(x=outlier$whole.gene.dN.dS.model.0,
y=outlier$dginn.primate_omegaM0Bpp,
outlier$Gene.name)
@
\subsection{Janet Young's results (Young-primate) VS Cooper's result}
Comparaison des Omega: colonne L "whole.gene.dN.dS.model.0" VS colonne "cooper.primates.Average\_dNdS".
<<omegaM7M8_2>>=
plot(tab$whole.gene.dN.dS.model.0, as.numeric(as.character(tab$cooper.primates.Average_dNdS)),
xlab="Omega Young-primate", ylab="Omega Cooper-primate")
<<omegaM7M8_2>>=
tab$cooper.primates.Average_dNdS<-as.numeric(as.character(
tab$cooper.primates.Average_dNdS))
plot(tab$whole.gene.dN.dS.model.0,
tab$cooper.primates.Average_dNdS,
xlab="Omega Young-primate",
ylab="Omega Cooper-primate",
cex=0.3)
abline(0,1)
abline(lm(as.numeric(as.character(tab$cooper.primates.Average_dNdS))~tab$whole.gene.dN.dS.model.0), col="red")
abline(lm(tab$cooper.primates.Average_dNdS~tab$whole.gene.dN.dS.model.0),
col="red")
outlier<-tab[tab$whole.gene.dN.dS.model.0<0.15 &
tab$cooper.primates.Average_dNdS>0.4,]
text(x=outlier$whole.gene.dN.dS.model.0,
y=outlier$cooper.primates.Average_dNdS,
outlier$Gene.name, cex=0.5)
outlier<-tab[tab$whole.gene.dN.dS.model.0<0.4 & tab$cooper.primates.Average_dNdS>0.5,]
outlier<-tab[tab$whole.gene.dN.dS.model.0<0.3 &
tab$cooper.primates.Average_dNdS>0.5,]
text(x=outlier$whole.gene.dN.dS.model.0,
y=outlier$cooper.primates.Average_dNdS,
outlier$Gene.name)
outlier$Gene.name, cex=0.5)
outlier<-tab[tab$whole.gene.dN.dS.model.0>0.3 &
tab$cooper.primates.Average_dNdS<0.1,]
text(x=outlier$whole.gene.dN.dS.model.0,
y=outlier$cooper.primates.Average_dNdS,
outlier$Gene.name, cex=0.5)
@
\subsection{Cooper's results (Cooper-primate) VS DGINN-full's results}
Comparaison des Omega: colonne "cooper.primates.Average\_dNdS" VS colonne "omega" dans la sortie de dginn.
<<omegaM7M8_3>>=
plot(tab$cooper.primates.Average_dNd, as.numeric(as.character(tab$dginn.primate_omegaM0Bpp)),
xlab="Omega Cooper-primate", ylab="DGINN-full's")
<<omegaM7M8_3>>=
plot(tab$cooper.primates.Average_dNd,
tab$dginn.primate_omegaM0Bpp,
xlab="Omega Cooper-primate",
ylab="DGINN-full's",
cex=0.3)
abline(0,1)
abline(lm(as.numeric(as.character(tab$dginn.primate_omegaM0Bpp))~tab$cooper.primates.Average_dNd), col="red")
abline(lm(tab$dginn.primate_omegaM0Bpp~tab$cooper.primates.Average_dNd), col="red")
outlier<-tab[tab$cooper.primates.Average_dNd<0.4 & tab$dginn.primate_omegaM0Bpp>0.5,]
outlier<-tab[tab$cooper.primates.Average_dNd<0.4 &
tab$dginn.primate_omegaM0Bpp>0.5,]
text(x=outlier$cooper.primates.Average_dNd,
y=outlier$dginn.primate_omegaM0Bpp,
outlier$Gene.name)
@
outlier$Gene.name, cex=0.5)
outlier<-tab[tab$cooper.primates.Average_dNd<0.1 &
tab$dginn.primate_omegaM0Bpp>0.3,]
text(x=outlier$cooper.primates.Average_dNd,
y=outlier$dginn.primate_omegaM0Bpp,
outlier$Gene.name, cex=0.5)
outlier<-tab[tab$cooper.primates.Average_dNd>0.7 &
tab$dginn.primate_omegaM0Bpp<0.3,]
text(x=outlier$cooper.primates.Average_dNd,
y=outlier$dginn.primate_omegaM0Bpp,
outlier$Gene.name, cex=0.5)
outlier<-tab[tab$cooper.primates.Average_dNd>0.45 &
tab$dginn.primate_omegaM0Bpp<0.2,]
text(x=outlier$cooper.primates.Average_dNd,
y=outlier$dginn.primate_omegaM0Bpp,
outlier$Gene.name, cex=0.5)
@
\section{Overlap}
\subsection{Mondrian}
<<mondrianprimates>>=
library(Mondrian)
#######
monddata<-as.data.frame(tab$Gene.name)
dim(monddata)
dginnfulltmp<-rowSums(cbind(tab$dginn.primate_BUSTED=="Y",
tab$dginn.primate_BppM1M2=="Y",
tab$dginn.primate_BppM7M8=="Y",
tab$dginn.primate_codemlM1M2=="Y",
tab$dginn.primate_codemlM7M8=="Y"))
dginnfulltmp<-rowSums(cbind(tab$dginn.primate_BUSTED=="Y", tab$dginn.primate_BppM1M2=="Y",
tab$dginn.primate_BppM7M8=="Y", tab$dginn.primate_codemlM1M2=="Y", tab$dginn.primate_codemlM7M8=="Y"))
monddata$primates_young<-ifelse(tab$pVal.M8vsM7<0.05, 1, 0)
monddata$primate_cooper<-ifelse(tab$cooper.primates.M7.M8_p_value<0.05, 1, 0)
monddata$primates_dginn_full<-ifelse(dginnfulltmp>=3, 1,0)
monddata$primates_young<-ifelse(
tab$pVal.M8vsM7<0.05, 1, 0)
monddata$primate_cooper<-ifelse(
tab$cooper.primates.M7.M8_p_value<0.05, 1, 0)
monddata$primates_dginn_full<-ifelse(
dginnfulltmp>=3, 1,0)
mondrian(na.omit(monddata[,2:4]), labels=c("Young", "Cooper", "DGINN-full >=3" ))
mondrian(na.omit(monddata[,2:4]),
labels=c("Young", "Cooper", "DGINN-full >=3" ))
#####
monddata$primates_dginn_full<-ifelse(dginnfulltmp>=4, 1,0)
monddata$primates_dginn_full<-ifelse(
dginnfulltmp>=4, 1,0)
mondrian(na.omit(monddata[,2:4]), labels=c("Young", "Cooper", "DGINN-full >=4"))
mondrian(na.omit(monddata[,2:4]),
labels=c("Young", "Cooper", "DGINN-full >=4"))
@
......@@ -144,7 +202,8 @@ library(UpSetR)
upsetdata<-as.data.frame(tab$Gene.name)
upsetdata$primates_young<-ifelse(tab$pVal.M8vsM7<0.05, 1, 0)
upsetdata$primate_cooper<-ifelse(tab$cooper.primates.M7.M8_p_value<0.05, 1, 0)
upsetdata$primate_cooper<-ifelse(
tab$cooper.primates.M7.M8_p_value<0.05, 1, 0)
upsetdata$primates_dginn_full<-ifelse(dginnfulltmp>=3, 1,0)
......
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